10-100372754-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693438.2(ENSG00000289301):n.640G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,016 control chromosomes in the GnomAD database, including 4,153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (4153 hom., cov: 32)
• Consequence: ENST00000693438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000693438.2	n.640G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29275 AN: 151898 Hom.: 4140 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 29320 AN: 152016 Hom.: 4153 Cov.: 32 AF XY: 0.192 AC XY: 14266 AN XY: 74302

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0994

Gnomad4 OTH AF: 0.157

Alfa AF: 0.129 Hom.: 437

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.74
Dann	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs569184; hg19: chr10-102132511;